Dens invaginatus is a malformation that can arise in any tooth, but cases in molars are rare. A young adult patient in good dental health presented with an extensive infection of his right maxilla, and a diagnosis of acute periodontal abscess was made. Further investigation revealed acute periapical periodontitis arising from a necrotic third molar pulp. With the tooth extracted, a rare and seldomly reported case of a maxillary third molar dens invaginatus was revealed. Micro CT is useful for studying this type of malformation.